[gmx-users] Question about documentation of -a switch in g_hbond
Justin A. Lemkul
jalemkul at vt.edu
Sun Jun 10 16:41:48 CEST 2012
On 6/10/12 10:36 AM, Andrew DeYoung wrote:
> This might end up being a silly/embarrassing question, and if so, I
> apologize. I feel like I may be making a conceptual mistake, but I'm not
> Is it true that a hydrogen bond is of the following form?
> Donor---Hydrogen ... Acceptor
> Is this the correct order? I think so. For example, in my system, I have:
> Oxygen---Hydrogen ... Fluorine
> In the documentation, the -a option has this description:
> "Cutoff angle (degrees, Acceptor - Donor - Hydrogen)"
> Why is the order Acceptor - Donor - Hydrogen (or, equivalently, Hydrogen -
> Donor - Acceptor)? Why isn't "Hydrogen" instead between "Donor" and
> "Acceptor"? Which angle does -a specify?
Because it's easy to define from an algorithmic standpoint. A hydrogen bond is
stronger depending on how close to linearity it is. Measuring an acute angle
given by -a says that if the A-D-H angle is less than 35 degrees, you can vary
between 0 and 35 easily to show the same thing as being within a certain range
of being 180 degrees in terms of D-H-A.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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